Meta-Analysis of RNA-Seq Datasets Identifies Novel Players in Glioblastoma

SIMPLE SUMMARY: Glioblastoma is a grade IV glioma of heterogeneous nature, which complicates disease pathophysiology and biomarker research. The aim of this meta-analysis was to identify long non-coding RNAs (lncRNAs) and protein-coding genes (PCGs) that are differentially expressed in glioblastoma. Additionally, small RNA-seq of glioblastoma tissues was performed to identify differentially expressed microRNAs (miRNAs) compared to normal tissue controls. The meta-analysis identified 98 and 360 differentially expressed lncRNAs (DElncRNAs) and PCGs (DEPCGs), respectively, in addition to five differentially expressed miRNAs (DEmiRNAs) identified by small RNA-seq. Co-expression correlation network clustering of DElncRNAs/DEPCGs identified a functionally relevant sub-cluster containing DANCR and SNHG6, with DElncRNAs overlapping with TCGA-GBM output. Analysis of the pathways associated with these DElncRNAs and DEPCGs revealed an association with a novel cell death pathway, ferroptosis. Thus, our results confirm the involvement of ferroptosis in glioblastoma pathophysiology and present several candidates for further research ABSTRACT: Glioblastoma is a devastating grade IV glioma with poor prognosis. Identification of predictive molecular biomarkers of disease progression would substantially contribute to better disease management. In the current study, we performed a meta-analysis of different RNA-seq datasets to identify differentially expressed protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs). This meta-analysis aimed to improve power and reproducibility of the individual studies while identifying overlapping disease-relevant pathways. We supplemented the meta-analysis with small RNA-seq on glioblastoma tissue samples to provide an overall transcriptomic view of glioblastoma. Co-expression correlation of filtered differentially expressed PCGs and lncRNAs identified a functionally relevant sub-cluster containing DANCR and SNHG6, with two novel lncRNAs and two novel PCGs. Small RNA-seq of glioblastoma tissues identified five differentially expressed microRNAs of which three interacted with the functionally relevant sub-cluster. Pathway analysis of this sub-cluster identified several glioblastoma-linked pathways, which were also previously associated with the novel cell death pathway, ferroptosis. In conclusion, the current meta-analysis strengthens evidence of an overarching involvement of ferroptosis in glioblastoma pathogenesis and also suggests some candidates for further analyses.